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1 process MASHTREE {
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2 tag "$meta.id"
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3 label 'process_medium'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mashtree${params.fs}1.4.3" : null)
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6 conda (params.enable_conda ? "bioconda::mashtree=1.4.3 conda-forge::perl conda-forge::coreutils" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/mashtree:1.4.3--pl5321h031d066_0' :
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9 'quay.io/biocontainers/mashtree:1.4.3--pl5321h031d066_0' }"
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10
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11 input:
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12 tuple val(meta), path(seqs)
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13 path reference
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14
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15 output:
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16 tuple val(meta), path("*.dnd"), emit: tree
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17 tuple val(meta), path("*.tsv"), emit: matrix
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18 tuple val(meta), path("*.nwk"), emit: nwk, optional: true
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19 path "versions.yml" , emit: versions
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20
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21 when:
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22 task.ext.when == null || task.ext.when
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23
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24 script:
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25 def args = task.ext.args ?: ''
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26 def prefix = task.ext.prefix ?: "${meta.id}"
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27 def fofn = (args.toString().matches(/.*file\-of\-files/) ? 'true' : 'false')
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28 def fas = reference.collect().join('\\n')
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29 def ref_fasta = (fas ?: '')
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30 """
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31
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32 echo -e "$ref_fasta" | while read -r fa; do
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33 if ! grep -F "\${fa}" $seqs && [ "$fofn" = "true" ]; then
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34 echo "\${fa}" >> $seqs
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35 fi
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36 done
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37
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38 mashtree \\
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39 $args \\
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40 --tempdir "." \\
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41 --numcpus $task.cpus \\
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42 --outmatrix ${prefix}.tsv \\
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43 --outtree ${prefix}.dnd \\
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44 $seqs
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45
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46 sed -ie 's/_scaffolded_genomic//g' ${prefix}.dnd
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47 cp ${prefix}.dnd ${prefix}.nwk
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48
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49 cat <<-END_VERSIONS > versions.yml
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50 "${task.process}":
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51 mashtree: \$( echo \$( mashtree --version 2>&1 ) | sed 's/^.*Mashtree //' )
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52 END_VERSIONS
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53
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54 sedver=""
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55 grepver=""
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56
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57 if [ "${workflow.containerEngine}" != "null" ]; then
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58 sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
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59 grepver="\$sedver"
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60 else
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61 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
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62 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
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63 fi
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64
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65 cat <<-END_VERSIONS >> versions.yml
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66 grep: \$grepver
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67 sed: \$sedver
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68 END_VERSIONS
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69 """
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70 } |
